How to grid search feature selection and neural network hyperparameters in the same grid?

Question

I'm using the GridSearchCV () class from scikit to perform hyperparameter optimization in a sequential neural network. I've built a pipeline to also find the best number of features by putting a feature selector inside the pipeline. The problem is how to define the input_shape, since this depends on the k parameter from the feature selector. Is it possible to set the value of classifier__input_shape to be the same value (at all times) of feature_selector__feature__selector_k?
I've provided the correspondent piece of code below.
def create_model (learn_rate = 0.01, dropout_rate = 0.0, weight_constraint = 0, input_shape):
  model = Sequential ()
  model.add (Dense (units = 64, activation = 'relu',
                   input_shape = (input_shape, )))
  model.add (Dropout (dropout_rate))
  model.add (Dense (32, activation = 'relu'))
  model.add (Dense (1, activation = 'sigmoid'))
  model.compile (loss = 'binary_crossentropy',
                optimizer = Adam (lr = learn_rate),
                metrics = ['accuracy'])#, metrics.CategoricalAccuracy ()])
  return model

standard_scaler_features = remaining_features
my_scaler = StandardScaler ()
steps = list ()
steps.append (('scaler', my_scaler))
standard_scaler_transformer = Pipeline (steps)

my_feature_selector = SelectKBest ()
steps = list ()
steps.append (('feature_selector', my_feature_selector))
feature_selector_transformer = Pipeline (steps)

clf = KerasClassifier (build_fn = create_model, verbose = 2)
clf = Pipeline (steps = [('scaler', my_scaler),
                         ('feature_selector', feature_selector_transformer),
                         ('classifier', clf)],
                verbose = True)

param_grid = {'feature_selector__feature_selector__score_func' : [f_classif],
              'feature_selector__feature_selector__k' : [7, 9, 15],
              'classifier__input_shape' : [7, 9, 15],
              'classifier__epochs' : [2, 3, 4]}
cv = RepeatedStratifiedKFold (n_splits = 5, n_repeats = 1, random_state = STATE)
grid = GridSearchCV (estimator = clf, param_grid = param_grid, scoring = 'f1',
                     verbose = 1, n_jobs = 1, cv = cv)
grid_result = grid.fit (X_train_df, y_train_df)

And the error:
ValueError: Input 0 of layer sequential_9 is incompatible with the layer: expected axis -1 of input shape to have value 9 but received input with shape [None, 7]

etiennedm · Accepted Answer

I see two solutions:

either you pass a list of dictionnaries to param_grid avoiding irrelevant combinations
or you use a single variable in your pipeline for feature_selector__feature__selector_k and classifier__input_shape

First solution:  you can generate the right list of combinations using something close to this:
param_grid = [
    {
        'feature_selector__feature_selector__score_func' : [f_classif],
        'feature_selector__feature_selector__k' : [k],
        'classifier__input_shape' : [k],
        'classifier__dropout_rate' : [0.0, 0.5]
    } 
    for k in [7, 9, 15] 
             ]

Second solution, you can use a specific class that create your model when fitting based on the shape of X. Here is a code sample:
class MyKerasClf():
    def predict(self, X):
        y_pred_nn = self.clf.predict(X)
        return np.array(y_pred_nn).flatten()
    
    def create_model(self, learn_rate = 0.01, weight_constraint = 0 ):
        model = Sequential ()
        model.add (Dense (units = 64, activation = 'relu',
                       input_shape = (self.input_shape, )))
        model.add (Dropout (self.dropout_rate))
        model.add (Dense (32, activation = 'relu'))
        model.add (Dense (1, activation = 'sigmoid'))
        model.compile (loss = 'binary_crossentropy',
                    optimizer = Adam (lr = learn_rate),
                    metrics = ['accuracy'])
        return model
        
    def fit(self, X, y, **kwargs):
        self.input_shape = X.shape[1]
        self.clf = KerasClassifier(build_fn = self.create_model, verbose = 2)
        self.clf.fit(X, y, **kwargs)
    
    def set_params(self, **params):
        if 'dropout_rate' in params:
            self.dropout_rate = params['dropout_rate']
        else:
            self.dropout_rate = 0.0

Then you can use the class in your pipeline
X, y = make_classification(n_features=50, n_redundant=0, n_informative=2,
                           random_state=42, n_clusters_per_class=1)

my_scaler = StandardScaler ()
steps = list ()
steps.append (('scaler', my_scaler))
standard_scaler_transformer = Pipeline (steps)

my_feature_selector = SelectKBest ()
steps = list ()
steps.append (('feature_selector', my_feature_selector))
feature_selector_transformer = Pipeline (steps)

# Create a specific clf
my_clf = MyKerasClf( )
pip_clf = Pipeline (steps = [('scaler', my_scaler),
                         ('feature_selector', feature_selector_transformer),
                         ('classifier', my_clf)],
                verbose = True)

param_grid = {'feature_selector__feature_selector__score_func' : [f_classif],
              'feature_selector__feature_selector__k' : [7, 15],
              'classifier__dropout_rate' : [0.0, 0.5]
             }
cv = RepeatedStratifiedKFold (n_splits = 5, n_repeats = 1, random_state = 42)
grid = GridSearchCV (estimator = pip_clf, param_grid = param_grid, scoring = 'f1',
                     verbose = 1, n_jobs = 1, cv = cv)
grid_result = grid.fit(X, y)

Note: I although added the dropout to be tested in the gridsearch as an example.

How to grid search feature selection and neural network hyperparameters in the same grid?

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